class BIDSFreeSurferDirInputSpec(BaseInterfaceInputSpec):
derivatives = Directory(exists=True, mandatory=True,
desc='BIDS derivatives directory')
freesurfer_home = Directory(exists=True, mandatory=True,
desc='FreeSurfer installation directory')
subjects_dir = traits.Str('freesurfer', usedefault=True,
desc='Name of FreeSurfer subjects directory')
spaces = traits.List(traits.Str, desc='Set of output spaces to prepare')
overwrite_fsaverage = traits.Bool(False, usedefault=True,
desc='Overwrite fsaverage directories, if present')
class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
t1w = InputMultiPath(File(exists=True), desc='T1w structural images')
t2w = InputMultiPath(File(exists=True), desc='T2w structural images')
subjects_dir = Directory(desc='FreeSurfer subjects directory')
subject_id = Str(desc='Subject ID')
bold = traits.List(desc='BOLD functional series')
output_spaces = traits.List(desc='Target spaces')
template = traits.Enum('MNI152NLin2009cAsym', desc='Template space')
class GenerateCiftiInputSpec(BaseInterfaceInputSpec):
bold_file = File(mandatory=True, exists=True, desc="input BOLD file")
volume_target = traits.Enum("MNI152NLin2009cAsym",
mandatory=True,
usedefault=True,
desc="CIFTI volumetric output space")
surface_target = traits.Enum("fsaverage5",
"fsaverage6",
mandatory=True,
usedefault=True,
desc="CIFTI surface target space")
subjects_dir = Directory(mandatory=True, desc="FreeSurfer SUBJECTS_DIR")
TR = traits.Float(mandatory=True, desc="repetition time")
gifti_files = traits.List(
File(exists=True),
mandatory=True,
desc="list of surface geometry files (length 2 with order [L,R])")
class ICAConfoundsInputSpec(BaseInterfaceInputSpec):
in_directory = Directory(mandatory=True,
desc='directory where ICA derivatives are found')
ignore_aroma_err = traits.Bool(False,
usedefault=True,
desc='ignore ICA-AROMA errors')
class FSInjectBrainExtractedOutputSpec(TraitedSpec):
subjects_dir = Directory(desc='FreeSurfer SUBJECTS_DIR')
subject_id = traits.Str(desc='Subject ID')
class FSInjectBrainExtractedInputSpec(BaseInterfaceInputSpec):
subjects_dir = Directory(mandatory=True, desc='FreeSurfer SUBJECTS_DIR')
subject_id = traits.Str(mandatory=True, desc='Subject ID')
in_brain = File(mandatory=True,
exists=True,
desc='input file, part of a BIDS tree')
class MedialNaNsInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='input surface file')
target_subject = traits.Str(mandatory=True, desc='target subject ID')
subjects_dir = Directory(mandatory=True, desc='FreeSurfer SUBJECTS_DIR')